Repositories list

• app-qsiprep

  Public
  Preprocessing of diffusion MRI data. It includes automatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, coregister and resample your scans, producing visual reports and QC metrics.

  pipelinepreprocessing

  Python

  •

  MIT License

  •9•3•2•0•Updated Nov 13, 2025Nov 13, 2025

• amaretti

  Public
  Lightweight task orchestration service for ABCD-specification compatible apps.

  JavaScript

  •

  MIT License

  •4•6•18•12•Updated Nov 5, 2025Nov 5, 2025

• warehouse

  Public
  Service that allows data warehousing and workfow orchestration

  CSS

  •

  MIT License

  •13•13•0•25•Updated Nov 5, 2025Nov 5, 2025

• brainlife.hugo

  Public
  Brainlife Hugo Setup

  HTML

  •7•1•0•1•Updated Nov 5, 2025Nov 5, 2025

• abcd-spec

  Public
  Application for Big Computational Data Specification (v1.1). This specification provide information on how to write an Application that can run on the open platform

  specificationcloud-computingbrain+ 3biomedical-image-processinghcpcyberinfrastructure

  Python

  •

  MIT License

  •8•10•6•1•Updated Oct 28, 2025Oct 28, 2025

• app-archive

  Public
  App responsible for archiving output datasets (experimental)

  Python

  •

  MIT License

  •0•1•0•1•Updated Oct 24, 2025Oct 24, 2025

• app-stage

  Public
  App used to stage datasets from archive

  Python

  •

  MIT License

  •0•1•0•0•Updated Oct 17, 2025Oct 17, 2025

• app-benson14-retinotopy

  Public
  Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

  Shell

  •

  MIT License

  •6•1•0•0•Updated Oct 14, 2025Oct 14, 2025

• validator-tif

  Public
  Python

  •1•0•0•0•Updated Sep 30, 2025Sep 30, 2025

• ga-launcher

  Public
  Group Analysis container Launcher (experimental)

  Shell

  •2•1•1•0•Updated Sep 29, 2025Sep 29, 2025

• auth

  Public
  Simple, generic authentication service API and UI that issues JWT token

  jwtauthentication

  JavaScript

  •

  MIT License

  •2•1•13•4•Updated Sep 18, 2025Sep 18, 2025

• event

  Public
  Simple Event Service (AMQP > WebSocket gateway)

  JavaScript

  •3•0•2•6•Updated Sep 4, 2025Sep 4, 2025

• ezbids

  Public
  A web service for semi-automated conversion of raw imaging data to BIDS

  webdicominteroperability+ 7mrineuroimagingbidsniftibrain-imagingdata-curationbids-converter

  Vue

  •

  MIT License

  •19•34•17•6•Updated Jul 16, 2025Jul 16, 2025

• app-FSLTopupEddy

  Public
  This app will correct for encoding, eddy currents, and motion artifacts using FSL's Topup and Eddy functions.

  preprocessing

  Shell

  •1•1•0•0•Updated Jun 9, 2025Jun 9, 2025

• app-fsl-anat

  Public
  Shell

  •0•1•0•0•Updated Jun 6, 2025Jun 6, 2025

• dockerfiles

  Public
  repository to store various dockerfiles used to build docker containers that are used across multiple brainlife apps

  Dockerfile

  •1•3•2•0•Updated May 19, 2025May 19, 2025

• ants-docker

  Public
  Dockerfile for ANTs 2.3.1 via Conda + HCP pipelines + MNI templates

  Dockerfile

  •0•0•0•0•Updated May 13, 2025May 13, 2025

• docs

  Public
  Brainlife.io Documentation

  documentationneuroscienceeducational+ 2neuroimagingbrainlife

  HTML

  •28•16•14•2•Updated Apr 16, 2025Apr 16, 2025

• validator-psoct

  Public
  Python

  •1•0•0•0•Updated Apr 8, 2025Apr 8, 2025

• app-fmriprep

  Public
  fMRIPrep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting.

  fmripreprocessing

  Shell

  •

  MIT License

  •10•3•10•1•Updated Mar 31, 2025Mar 31, 2025

• app-ensembletracking

  Public
  This App creates a large set of candidate streamlines using an ensemble of algorithms and parameter values. All outputs will be then combined into a single track.tck output.

  tracking

  Shell

  •1•0•6•0•Updated Mar 24, 2025Mar 24, 2025

• pybrainlife

  Public
  Library to access brainlife.io data objects and jupyter notebooks

  python3jupyterlabjupyter-notebooks+ 1brainlifeio

  Python

  •0•4•1•2•Updated Mar 14, 2025Mar 14, 2025

• ui-networkneuro-tracts

  Public
  networkneuro fiber/roi visualizer

  JavaScript

  •0•1•0•1•Updated Mar 6, 2025Mar 6, 2025

• app-cortex-tissue-mapping-stats

  Public
  Shell

  •

  MIT License

  •1•2•4•1•Updated Dec 19, 2024Dec 19, 2024

• app-freesurfer-stats

  Public
  Python

  •1•1•5•1•Updated Dec 19, 2024Dec 19, 2024

• app-visual-white-matter

  Public
  Shell

  •2•1•0•0•Updated Dec 5, 2024Dec 5, 2024

• app-hcp-acpc-alignment

  Public
  This app will align a T1w image to the ACPC plane (specifically, the MNI152_T1_1mm template from FSL using a 6 DOF alignment via FSL commands. This protocol was adapted from the HCP Preprocessing Pipeline (https://github.com/Washington-University/HCPpipelines.git). Requires a T1w image input and outputs an acpc_aligned T1w image.

  anatomy-preprocessing

  Shell

  •

  MIT License

  •4•8•3•1•Updated Nov 11, 2024Nov 11, 2024

• validator-fmap

  Public
  fieldmap datatype validator

  Python

  •1•1•0•0•Updated Oct 30, 2024Oct 30, 2024

• ui-niivue

  Public
  HTML

  •0•1•1•0•Updated Sep 13, 2024Sep 13, 2024

• app-predict-ppcs

  Public
  App to predict Persisting Post Concussion Symptoms

  Python

  •

  MIT License

  •0•1•0•0•Updated Jun 29, 2024Jun 29, 2024